Paper- RNA-seq of tumor-educated platelets enables blood-based

Added on - 16 Sep 2019

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Paper-RNA-seq of tumor-educated platelets enables blood-based pan-cancer, multiclass andmolecular pathway cancer diagnostics”http://www.cell.com/action/showMethods?pii=S1535-6108%2815%2900349-9Data-https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE68086I would like to do a comparison of methods for analyzing the RNA-Seq data in Myron G.Bestet.al’s paper . The paper focused on Tumor-educated-blood platelets and their role in tumorgrowth They sequences 283 platelets from 6 difference tumor types. The primary tumor wascorrectly identified 71% of the time. There results show that blood platelets can give anindication of where the cancer will be found and can provide diagnostic advances in oncology.The data was analyzed by using voom. This will be under the limma package that we have used.I want to compare the analysis with edgeR and DESeq2. I believe seeing the similarities anddifferences in the type of analysis will show how important methodology is I reproducing anexperiment.Method:Normalize and perform QC of the DataedgeR differential expression analysisvoom differential expression analysis and comparison to results in the paper.DESeq2 differential expression analysis.The last part is the comparison of the three methodologies. I will show similarities , differencesand which method worked the best in finding more differentially expressed genes.